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Job request: 2302

Workspace:
post-covid-competing-risks
ID:
4nhcveo7escwsoyc

This page shows the technical details of what happened when authorised researcher John Tazare requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml
version: "3.0"

expectations:
  population_size: 20000

actions:
  generate_covid_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
    outputs:
      highly_sensitive:
        cohort: output/input_covid.csv

  generate_covid_community_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
    outputs:
      highly_sensitive:
        cohort: output/input_covid_community.csv

  generate_covid_general_population_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population
    outputs:
      highly_sensitive:
        cohort: output/input_general_population.csv

  generate_pneumonia_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
    outputs:
      highly_sensitive:
        cohort: output/input_pneumonia.csv

  matching:
    run: python:latest python analysis/match_running.py
    needs: [generate_covid_cohort, generate_covid_general_population_cohort]
    outputs:
      moderately_sensitive: 
        matching_report: output/matching_report_general_population.txt  
      highly_sensitive: 
        combined: output/matched_combined_general_population.csv

  covid_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_covid_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta
      moderately_sensitive:
        out_dist: output/tabfig/outcomes_in_hosp_covid.csv

  covid_community_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
    needs: [generate_covid_community_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid_community.dta

  pneumonia_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_pneumonia_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta
      moderately_sensitive:
        out_dist: output/tabfig/outcomes_in_hosp_pneumonia.csv

  gen_pop_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "matched_combined_general_population"
    needs: [matching]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_gen_population.dta

  covid_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [covid_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid.csv

  covid_comm_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
    needs: [covid_community_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_community.csv

  pneumonia_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_pneumonia.csv

  gen_pop_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "gen_population"
    needs: [gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_gen_population.csv

  baseline_characteristics:
    run: stata-mp:latest analysis/400_baseline_characteristics.do
    needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        tables: output/tabfig/an_descriptiveTable_*.txt

  append_cohorts:
    run: stata-mp:latest analysis/300_cr_data_management_matching.do
    needs: [covid_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        log: output/append_cohorts.txt
      highly_sensitive: 
        dataset: output/combined_covid_pneumonia.dta
        dataset2: output/combined_covid_gen_population.dta

  cox_models:
    run: stata-mp:latest analysis/302_cox_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cox_models.txt
        dataset: output/tabfig/cox_model_summary.csv


  fine_gray:
    run: stata-mp:latest analysis/302_competing_events.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/competing_events.txt
        dataset: output/tabfig/fine_gray_summary.csv
        figs: output/tabfig/cumInc_*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

These timestamps are generated and stored using the UTC timezone on the backend.

Job information

Status
Failed
Completed successfully
Backend
TPP
Requested by
John Tazare
Branch
reviewer-updates
Force run dependencies
Yes
Git commit hash
ee6e8d4
Requested actions
  • generate_covid_cohort
  • generate_covid_community_cohort
  • generate_covid_general_population_cohort
  • generate_pneumonia_cohort
  • matching
  • covid_rates_cohort
  • covid_community_rates_cohort
  • pneumonia_rates_cohort
  • gen_pop_rates_cohort
  • covid_rates
  • covid_comm_rates
  • pneumonia_rates
  • gen_pop_rates
  • baseline_characteristics
  • append_cohorts
  • cox_models
  • fine_gray
  • run_all